Article ID: 1440 - Last Modified: April 19, 2011

How do I replace a loop in structure A with one from Structure B?

Use the Prime Structure Prediction workflow.

In order to build the loop B residue types, and not just the loop conformation, the structure A query sequence will have to have the sequence of the desired loop replaced with the loop sequence from B.

Read in your (modified) query sequence from structure A.

Import first structure B, then structure A as homologs in the Find Homologs step.
Structure A should now be the top template.

Make sure Structure A and B are aligned (you can align them in the Find Homologs step if they are not already aligned).

Do further alignment of the sequences, if necessary, in the Edit Alignment step, and then go to the Build Structure step.

Click the Set Template Regions button (the one with two rows of AAA on it)

By default, Prime will build the query on the top template (should be template A in this case)

Mark the desired loop residues to use from structure B in the structure B template sequence (drag over the desired residues in the sequence viewer).

You will see that the residues in the structure B loop are highlighted, while the corresponding residues in structure A are grayed out.

Include ligands or co-factors if present (and desired), then click Build.

Once the structure is built, you can place it in the project table and use the Prime Refinement panel to perform loop sampling on the built loop.